8Q00
TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.06 | 49.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.75 | α = 90 |
| b = 103.75 | β = 90 |
| c = 191.52 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | default | 2021-05-11 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.00000 | SLS | X06SA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
| 1 | 1.62 | 103.74 | 99.9 | 0.076 | 0.08 | 0.9990000000000001 | 18.54 | 13.42 | 132701 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.62 | 1.66 | 2.335 | 2.425 | 0.516 | 1.19 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.62 | 91.22 | 130701 | 2000 | 99.95 | 0.17473 | 0.17436 | 0.19822 | RANDOM | 28.719 | |||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.47 | 0.47 | -0.94 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 13.039 |
| r_dihedral_angle_2_deg | 10.686 |
| r_long_range_B_refined | 8.062 |
| r_long_range_B_other | 8.013 |
| r_scangle_other | 6.612 |
| r_dihedral_angle_1_deg | 6.267 |
| r_scbond_it | 4.536 |
| r_scbond_other | 4.536 |
| r_mcangle_it | 3.787 |
| r_mcangle_other | 3.787 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5704 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 724 |
| Heterogen Atoms | 23 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHENIX | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| PHASER | phasing |
